Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.14

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-02-09, 00:06 CET based on data in:

        General Statistics

        Showing 328/328 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        SRR13434505_qc_fHP_1
        25.7%
        49%
        150 bp
        14.4
        SRR13434505_qc_fHP_2
        25.0%
        49%
        148 bp
        14.4
        SRR13434506_qc_fHP_1
        11.7%
        51%
        150 bp
        15.9
        SRR13434506_qc_fHP_2
        11.0%
        51%
        148 bp
        15.9
        SRR13434507_qc_fHP_1
        14.2%
        47%
        150 bp
        14.9
        SRR13434507_qc_fHP_2
        13.7%
        47%
        144 bp
        14.9
        SRR13434508_qc_fHP_1
        23.8%
        51%
        150 bp
        16.7
        SRR13434508_qc_fHP_2
        21.3%
        51%
        150 bp
        16.7
        SRR13434509_qc_fHP_1
        15.6%
        50%
        150 bp
        15.4
        SRR13434509_qc_fHP_2
        14.7%
        50%
        150 bp
        15.4
        SRR13434510_qc_fHP_1
        13.6%
        53%
        150 bp
        14.4
        SRR13434510_qc_fHP_2
        13.0%
        53%
        142 bp
        14.4
        SRR13434511_qc_fHP_1
        17.4%
        50%
        150 bp
        18.6
        SRR13434511_qc_fHP_2
        16.6%
        50%
        144 bp
        18.6
        SRR13434512_qc_fHP_1
        22.9%
        48%
        150 bp
        19.1
        SRR13434512_qc_fHP_2
        22.3%
        48%
        144 bp
        19.1
        SRR13434513_qc_fHP_1
        27.4%
        49%
        150 bp
        20.1
        SRR13434513_qc_fHP_2
        26.1%
        49%
        146 bp
        20.1
        SRR13434514_qc_fHP_1
        14.3%
        50%
        150 bp
        10.6
        SRR13434514_qc_fHP_2
        13.5%
        49%
        144 bp
        10.6
        SRR13434516_qc_fHP_1
        15.1%
        47%
        150 bp
        13.3
        SRR13434516_qc_fHP_2
        14.2%
        47%
        148 bp
        13.3
        SRR13434517_qc_fHP_1
        14.7%
        49%
        150 bp
        13.1
        SRR13434517_qc_fHP_2
        14.0%
        48%
        148 bp
        13.1
        SRR13434518_qc_fHP_1
        13.8%
        49%
        150 bp
        16.5
        SRR13434518_qc_fHP_2
        13.3%
        49%
        136 bp
        16.5
        SRR13434519_qc_fHP_1
        11.8%
        48%
        150 bp
        11.4
        SRR13434519_qc_fHP_2
        11.4%
        48%
        142 bp
        11.4
        SRR13434520_qc_fHP_1
        14.9%
        51%
        150 bp
        15.6
        SRR13434520_qc_fHP_2
        14.0%
        51%
        146 bp
        15.6
        SRR13434521_qc_fHP_1
        16.6%
        48%
        150 bp
        17.1
        SRR13434521_qc_fHP_2
        15.7%
        48%
        150 bp
        17.1
        SRR13434522_qc_fHP_1
        16.1%
        50%
        150 bp
        15.7
        SRR13434522_qc_fHP_2
        15.2%
        50%
        148 bp
        15.7
        SRR13434523_qc_fHP_1
        17.4%
        51%
        150 bp
        13.4
        SRR13434523_qc_fHP_2
        16.6%
        51%
        144 bp
        13.4
        SRR13434524_qc_fHP_1
        13.1%
        54%
        124 bp
        20.9
        SRR13434524_qc_fHP_2
        13.9%
        54%
        124 bp
        20.9
        SRR13434525_qc_fHP_1
        6.6%
        49%
        124 bp
        9.3
        SRR13434525_qc_fHP_2
        7.1%
        49%
        124 bp
        9.3
        SRR13434527_qc_fHP_1
        9.0%
        52%
        124 bp
        7.8
        SRR13434527_qc_fHP_2
        9.9%
        52%
        124 bp
        7.8
        SRR13434528_qc_fHP_1
        12.6%
        52%
        124 bp
        16.8
        SRR13434528_qc_fHP_2
        13.5%
        52%
        124 bp
        16.8
        SRR13434529_qc_fHP_1
        14.6%
        51%
        124 bp
        12.4
        SRR13434529_qc_fHP_2
        14.7%
        51%
        124 bp
        12.4
        SRR13434530_qc_fHP_1
        13.9%
        49%
        124 bp
        18.6
        SRR13434530_qc_fHP_2
        14.0%
        49%
        124 bp
        18.6
        SRR13434531_qc_fHP_1
        11.8%
        51%
        124 bp
        11.5
        SRR13434531_qc_fHP_2
        12.5%
        51%
        124 bp
        11.5
        SRR13434532_qc_fHP_1
        15.4%
        50%
        124 bp
        23.3
        SRR13434532_qc_fHP_2
        15.6%
        50%
        124 bp
        23.3
        SRR13434533_qc_fHP_1
        20.2%
        50%
        124 bp
        17.2
        SRR13434533_qc_fHP_2
        20.2%
        50%
        124 bp
        17.2
        SRR13434534_qc_fHP_1
        20.4%
        53%
        124 bp
        16.4
        SRR13434534_qc_fHP_2
        20.6%
        53%
        124 bp
        16.4
        SRR13434535_qc_fHP_1
        12.0%
        50%
        124 bp
        13.3
        SRR13434535_qc_fHP_2
        12.1%
        50%
        124 bp
        13.3
        SRR13434536_qc_fHP_1
        15.1%
        49%
        124 bp
        17.1
        SRR13434536_qc_fHP_2
        14.5%
        49%
        124 bp
        17.1
        SRR13434538_qc_fHP_1
        13.9%
        50%
        124 bp
        15.7
        SRR13434538_qc_fHP_2
        13.7%
        50%
        124 bp
        15.7
        SRR13434539_qc_fHP_1
        11.3%
        50%
        124 bp
        14.1
        SRR13434539_qc_fHP_2
        11.5%
        50%
        124 bp
        14.1
        SRR13434540_qc_fHP_1
        11.3%
        50%
        124 bp
        15.6
        SRR13434540_qc_fHP_2
        11.3%
        50%
        124 bp
        15.6
        SRR13434541_qc_fHP_1
        11.9%
        52%
        124 bp
        15.9
        SRR13434541_qc_fHP_2
        12.0%
        52%
        124 bp
        15.9
        SRR13434542_qc_fHP_1
        13.0%
        47%
        124 bp
        15.7
        SRR13434542_qc_fHP_2
        14.0%
        47%
        124 bp
        15.7
        SRR13434543_qc_fHP_1
        15.0%
        49%
        124 bp
        21.2
        SRR13434543_qc_fHP_2
        16.7%
        49%
        124 bp
        21.2
        SRR13434544_qc_fHP_1
        7.7%
        51%
        124 bp
        14.2
        SRR13434544_qc_fHP_2
        9.0%
        51%
        124 bp
        14.2
        SRR13434545_qc_fHP_1
        11.3%
        48%
        124 bp
        20.4
        SRR13434545_qc_fHP_2
        12.8%
        48%
        124 bp
        20.4
        SRR13434546_qc_fHP_1
        10.6%
        50%
        124 bp
        18.8
        SRR13434546_qc_fHP_2
        12.0%
        50%
        124 bp
        18.8
        SRR13434547_qc_fHP_1
        17.9%
        52%
        112 bp
        11.2
        SRR13434547_qc_fHP_2
        19.9%
        52%
        112 bp
        11.2
        SRR13434549_qc_fHP_1
        9.1%
        51%
        124 bp
        11.8
        SRR13434549_qc_fHP_2
        10.3%
        51%
        124 bp
        11.8
        SRR13434550_qc_fHP_1
        12.7%
        50%
        124 bp
        17.5
        SRR13434550_qc_fHP_2
        13.9%
        50%
        124 bp
        17.5
        SRR13434551_qc_fHP_1
        8.1%
        50%
        124 bp
        17.6
        SRR13434551_qc_fHP_2
        8.8%
        50%
        124 bp
        17.6
        SRR13434552_qc_fHP_1
        8.3%
        51%
        124 bp
        9.5
        SRR13434552_qc_fHP_2
        9.8%
        51%
        124 bp
        9.5
        SRR13434553_qc_fHP_1
        17.5%
        51%
        124 bp
        19.1
        SRR13434553_qc_fHP_2
        18.4%
        51%
        124 bp
        19.1
        SRR13434554_qc_fHP_1
        16.7%
        51%
        124 bp
        16.7
        SRR13434554_qc_fHP_2
        18.7%
        51%
        124 bp
        16.7
        SRR13434555_qc_fHP_1
        17.0%
        52%
        124 bp
        12.9
        SRR13434555_qc_fHP_2
        19.0%
        52%
        124 bp
        12.9
        SRR13434556_qc_fHP_1
        15.5%
        51%
        124 bp
        18.2
        SRR13434556_qc_fHP_2
        17.0%
        51%
        124 bp
        18.2
        SRR13434557_qc_fHP_1
        10.3%
        51%
        124 bp
        16.3
        SRR13434557_qc_fHP_2
        11.6%
        51%
        124 bp
        16.3
        SRR13434558_qc_fHP_1
        9.6%
        52%
        124 bp
        17.9
        SRR13434558_qc_fHP_2
        11.0%
        52%
        124 bp
        17.9
        SRR13434560_qc_fHP_1
        10.2%
        52%
        124 bp
        14.6
        SRR13434560_qc_fHP_2
        11.5%
        52%
        124 bp
        14.6
        SRR13434561_qc_fHP_1
        9.9%
        50%
        124 bp
        14.0
        SRR13434561_qc_fHP_2
        11.2%
        50%
        124 bp
        14.0
        SRR13434562_qc_fHP_1
        19.0%
        52%
        124 bp
        23.8
        SRR13434562_qc_fHP_2
        20.1%
        52%
        124 bp
        23.8
        SRR13434563_qc_fHP_1
        12.6%
        51%
        124 bp
        19.7
        SRR13434563_qc_fHP_2
        13.7%
        51%
        124 bp
        19.7
        SRR13434564_qc_fHP_1
        14.1%
        52%
        124 bp
        19.1
        SRR13434564_qc_fHP_2
        15.1%
        52%
        124 bp
        19.1
        SRR13434565_qc_fHP_1
        12.1%
        52%
        124 bp
        14.4
        SRR13434565_qc_fHP_2
        13.4%
        52%
        124 bp
        14.4
        SRR13434566_qc_fHP_1
        8.6%
        52%
        124 bp
        15.5
        SRR13434566_qc_fHP_2
        9.6%
        52%
        124 bp
        15.5
        SRR13434567_qc_fHP_1
        14.7%
        52%
        124 bp
        15.5
        SRR13434567_qc_fHP_2
        16.2%
        52%
        124 bp
        15.5
        SRR13434568_qc_fHP_1
        13.4%
        52%
        124 bp
        11.0
        SRR13434568_qc_fHP_2
        13.9%
        52%
        124 bp
        11.0
        SRR13434569_qc_fHP_1
        19.0%
        52%
        124 bp
        22.2
        SRR13434569_qc_fHP_2
        19.1%
        52%
        124 bp
        22.2
        SRR13434571_qc_fHP_1
        13.9%
        51%
        124 bp
        17.5
        SRR13434571_qc_fHP_2
        14.2%
        51%
        124 bp
        17.5
        SRR13434572_qc_fHP_1
        16.4%
        52%
        124 bp
        20.4
        SRR13434572_qc_fHP_2
        16.6%
        52%
        124 bp
        20.4
        SRR13434573_qc_fHP_1
        14.7%
        51%
        124 bp
        24.6
        SRR13434573_qc_fHP_2
        15.1%
        51%
        122 bp
        24.6
        SRR13434574_qc_fHP_1
        10.8%
        51%
        124 bp
        18.2
        SRR13434574_qc_fHP_2
        11.2%
        51%
        124 bp
        18.2
        SRR13434575_qc_fHP_1
        11.9%
        52%
        124 bp
        13.8
        SRR13434575_qc_fHP_2
        13.6%
        52%
        124 bp
        13.8
        SRR13434576_qc_fHP_1
        16.9%
        50%
        124 bp
        15.3
        SRR13434576_qc_fHP_2
        18.7%
        50%
        124 bp
        15.3
        SRR13434577_qc_fHP_1
        11.6%
        52%
        124 bp
        13.7
        SRR13434577_qc_fHP_2
        13.3%
        52%
        124 bp
        13.7
        SRR13434578_qc_fHP_1
        5.2%
        48%
        124 bp
        7.2
        SRR13434578_qc_fHP_2
        6.3%
        48%
        124 bp
        7.2
        SRR13434579_qc_fHP_1
        8.9%
        52%
        124 bp
        10.4
        SRR13434579_qc_fHP_2
        10.5%
        52%
        124 bp
        10.4
        SRR13434580_qc_fHP_1
        12.3%
        49%
        124 bp
        20.3
        SRR13434580_qc_fHP_2
        14.4%
        49%
        124 bp
        20.3
        SRR13434582_qc_fHP_1
        14.5%
        53%
        104 bp
        17.5
        SRR13434582_qc_fHP_2
        14.2%
        53%
        100 bp
        17.5
        SRR13434583_qc_fHP_1
        17.0%
        52%
        108 bp
        17.1
        SRR13434583_qc_fHP_2
        16.5%
        52%
        104 bp
        17.1
        SRR13434584_qc_fHP_1
        19.9%
        49%
        120 bp
        19.8
        SRR13434584_qc_fHP_2
        18.8%
        49%
        110 bp
        19.8
        SRR13434585_qc_fHP_1
        21.8%
        52%
        124 bp
        35.8
        SRR13434585_qc_fHP_2
        21.8%
        52%
        124 bp
        35.8
        SRR13434586_qc_fHP_1
        13.5%
        51%
        124 bp
        15.1
        SRR13434586_qc_fHP_2
        13.3%
        51%
        124 bp
        15.1
        SRR13434587_qc_fHP_1
        14.4%
        51%
        124 bp
        23.5
        SRR13434587_qc_fHP_2
        14.3%
        51%
        124 bp
        23.5
        SRR13434591_qc_fHP_1
        28.1%
        50%
        150 bp
        26.3
        SRR13434591_qc_fHP_2
        26.7%
        50%
        150 bp
        26.3
        SRR13434592_qc_fHP_1
        17.7%
        52%
        136 bp
        11.2
        SRR13434592_qc_fHP_2
        17.2%
        52%
        134 bp
        11.2
        SRR13434595_qc_fHP_1
        13.7%
        52%
        150 bp
        9.6
        SRR13434595_qc_fHP_2
        13.1%
        52%
        150 bp
        9.6
        SRR13434597_qc_fHP_1
        18.3%
        53%
        132 bp
        11.5
        SRR13434597_qc_fHP_2
        17.8%
        53%
        132 bp
        11.5
        SRR13434598_qc_fHP_1
        21.0%
        46%
        150 bp
        29.4
        SRR13434598_qc_fHP_2
        19.8%
        46%
        150 bp
        29.4
        SRR13434599_qc_fHP_1
        21.8%
        48%
        150 bp
        33.7
        SRR13434599_qc_fHP_2
        20.9%
        48%
        150 bp
        33.7
        SRR13434600_qc_fHP_1
        23.6%
        47%
        150 bp
        25.2
        SRR13434600_qc_fHP_2
        22.3%
        47%
        150 bp
        25.2
        SRR13434601_qc_fHP_1
        15.7%
        51%
        72 bp
        5.0
        SRR13434601_qc_fHP_2
        15.4%
        51%
        72 bp
        5.0
        SRR13434602_qc_fHP_1
        19.2%
        50%
        136 bp
        9.3
        SRR13434602_qc_fHP_2
        18.7%
        50%
        134 bp
        9.3
        SRR13434603_qc_fHP_1
        16.2%
        49%
        150 bp
        24.1
        SRR13434603_qc_fHP_2
        15.3%
        49%
        150 bp
        24.1
        SRR13434604_qc_fHP_1
        26.1%
        51%
        150 bp
        38.7
        SRR13434604_qc_fHP_2
        24.0%
        51%
        150 bp
        38.7
        SRR13434605_qc_fHP_1
        20.8%
        54%
        150 bp
        32.9
        SRR13434605_qc_fHP_2
        18.6%
        54%
        150 bp
        32.9
        SRR13434606_qc_fHP_1
        20.2%
        49%
        150 bp
        23.4
        SRR13434606_qc_fHP_2
        18.4%
        49%
        150 bp
        23.4
        SRR13434609_qc_fHP_1
        15.3%
        48%
        150 bp
        25.5
        SRR13434609_qc_fHP_2
        14.7%
        48%
        150 bp
        25.5
        SRR13434610_qc_fHP_1
        21.1%
        48%
        150 bp
        38.9
        SRR13434610_qc_fHP_2
        19.6%
        48%
        150 bp
        38.9
        SRR13434611_qc_fHP_1
        19.9%
        50%
        150 bp
        31.2
        SRR13434611_qc_fHP_2
        18.2%
        50%
        150 bp
        31.2
        SRR13434612_qc_fHP_1
        18.6%
        48%
        150 bp
        13.5
        SRR13434612_qc_fHP_2
        17.8%
        48%
        150 bp
        13.5
        SRR13434614_qc_fHP_1
        23.1%
        53%
        150 bp
        32.2
        SRR13434614_qc_fHP_2
        21.8%
        53%
        150 bp
        32.2
        SRR13434615_qc_fHP_1
        14.6%
        51%
        104 bp
        11.7
        SRR13434615_qc_fHP_2
        14.3%
        51%
        104 bp
        11.7
        SRR13434616_qc_fHP_1
        9.2%
        50%
        72 bp
        5.4
        SRR13434616_qc_fHP_2
        9.1%
        50%
        72 bp
        5.4
        SRR13434617_qc_fHP_1
        17.3%
        53%
        150 bp
        18.0
        SRR13434617_qc_fHP_2
        15.9%
        54%
        150 bp
        18.0
        SRR13434618_qc_fHP_1
        17.1%
        53%
        150 bp
        20.5
        SRR13434618_qc_fHP_2
        15.4%
        53%
        150 bp
        20.5
        SRR13434620_qc_fHP_1
        29.1%
        42%
        150 bp
        15.8
        SRR13434620_qc_fHP_2
        28.1%
        42%
        150 bp
        15.8
        SRR13434621_qc_fHP_1
        19.9%
        43%
        104 bp
        8.2
        SRR13434621_qc_fHP_2
        19.8%
        43%
        104 bp
        8.2
        SRR13434622_qc_fHP_1
        20.5%
        44%
        150 bp
        15.7
        SRR13434622_qc_fHP_2
        19.6%
        44%
        150 bp
        15.7
        SRR13434623_qc_fHP_1
        15.2%
        48%
        150 bp
        21.1
        SRR13434623_qc_fHP_2
        13.5%
        48%
        150 bp
        21.1
        SRR13434624_qc_fHP_1
        17.7%
        48%
        150 bp
        23.8
        SRR13434624_qc_fHP_2
        16.0%
        47%
        150 bp
        23.8
        SRR13434625_qc_fHP_1
        18.3%
        49%
        150 bp
        20.6
        SRR13434625_qc_fHP_2
        16.7%
        49%
        150 bp
        20.6
        SRR13434626_qc_fHP_1
        17.0%
        47%
        132 bp
        13.5
        SRR13434626_qc_fHP_2
        16.6%
        47%
        128 bp
        13.5
        SRR13434627_qc_fHP_1
        23.9%
        45%
        150 bp
        9.9
        SRR13434627_qc_fHP_2
        23.0%
        45%
        144 bp
        9.9
        SRR13434628_qc_fHP_1
        13.0%
        49%
        150 bp
        11.4
        SRR13434628_qc_fHP_2
        12.4%
        49%
        144 bp
        11.4
        SRR13434629_qc_fHP_1
        15.3%
        52%
        150 bp
        25.4
        SRR13434629_qc_fHP_2
        13.2%
        52%
        150 bp
        25.4
        SRR13434631_qc_fHP_1
        14.5%
        53%
        150 bp
        22.8
        SRR13434631_qc_fHP_2
        13.2%
        53%
        150 bp
        22.8
        SRR13434632_qc_fHP_1
        19.9%
        52%
        150 bp
        30.6
        SRR13434632_qc_fHP_2
        18.1%
        52%
        150 bp
        30.6
        SRR13434633_qc_fHP_1
        23.4%
        49%
        150 bp
        30.1
        SRR13434633_qc_fHP_2
        21.9%
        49%
        150 bp
        30.1
        SRR13434634_qc_fHP_1
        20.2%
        50%
        150 bp
        22.6
        SRR13434634_qc_fHP_2
        18.6%
        50%
        150 bp
        22.6
        SRR13434643_qc_fHP_1
        22.8%
        51%
        150 bp
        26.6
        SRR13434643_qc_fHP_2
        21.1%
        51%
        150 bp
        26.6
        SRR13434644_qc_fHP_1
        19.8%
        53%
        150 bp
        21.1
        SRR13434644_qc_fHP_2
        18.2%
        53%
        150 bp
        21.1
        SRR13434645_qc_fHP_1
        30.2%
        51%
        150 bp
        23.3
        SRR13434645_qc_fHP_2
        27.4%
        51%
        150 bp
        23.3
        SRR13434646_qc_fHP_1
        22.7%
        48%
        150 bp
        23.5
        SRR13434646_qc_fHP_2
        20.9%
        48%
        150 bp
        23.5
        SRR13434647_qc_fHP_1
        28.7%
        46%
        150 bp
        24.6
        SRR13434647_qc_fHP_2
        26.8%
        46%
        150 bp
        24.6
        SRR13434649_qc_fHP_1
        23.2%
        49%
        150 bp
        29.0
        SRR13434649_qc_fHP_2
        21.6%
        49%
        150 bp
        29.0
        SRR13434654_qc_fHP_1
        20.7%
        48%
        150 bp
        23.7
        SRR13434654_qc_fHP_2
        19.6%
        48%
        150 bp
        23.7
        SRR13434655_qc_fHP_1
        19.7%
        49%
        150 bp
        22.3
        SRR13434655_qc_fHP_2
        18.0%
        49%
        150 bp
        22.3
        SRR13434662_qc_fHP_1
        21.0%
        50%
        150 bp
        19.0
        SRR13434662_qc_fHP_2
        18.7%
        50%
        150 bp
        19.0
        SRR13434665_qc_fHP_1
        21.7%
        46%
        150 bp
        22.4
        SRR13434665_qc_fHP_2
        19.6%
        46%
        150 bp
        22.4
        SRR13434666_qc_fHP_1
        24.2%
        49%
        150 bp
        28.2
        SRR13434666_qc_fHP_2
        22.2%
        49%
        150 bp
        28.2
        SRR13434667_qc_fHP_1
        18.4%
        50%
        150 bp
        27.0
        SRR13434667_qc_fHP_2
        16.5%
        50%
        150 bp
        27.0
        SRR13434668_qc_fHP_1
        10.9%
        51%
        122 bp
        7.1
        SRR13434668_qc_fHP_2
        10.6%
        51%
        120 bp
        7.1
        SRR13434669_qc_fHP_1
        24.1%
        49%
        150 bp
        15.7
        SRR13434669_qc_fHP_2
        22.9%
        49%
        150 bp
        15.7
        SRR13434670_qc_fHP_1
        20.3%
        54%
        142 bp
        10.4
        SRR13434670_qc_fHP_2
        19.5%
        54%
        136 bp
        10.4
        SRR13434671_qc_fHP_1
        18.1%
        51%
        150 bp
        16.4
        SRR13434671_qc_fHP_2
        16.3%
        51%
        150 bp
        16.4
        SRR13434673_qc_fHP_1
        9.3%
        47%
        76 bp
        4.0
        SRR13434673_qc_fHP_2
        9.1%
        47%
        76 bp
        4.0
        SRR13434675_qc_fHP_1
        18.6%
        47%
        150 bp
        18.0
        SRR13434675_qc_fHP_2
        17.3%
        47%
        150 bp
        18.0
        SRR13434676_qc_fHP_1
        19.7%
        49%
        150 bp
        26.9
        SRR13434676_qc_fHP_2
        18.0%
        49%
        150 bp
        26.9
        SRR13434677_qc_fHP_1
        31.2%
        45%
        150 bp
        21.4
        SRR13434677_qc_fHP_2
        29.5%
        45%
        150 bp
        21.4
        SRR13434680_qc_fHP_1
        24.4%
        47%
        150 bp
        24.6
        SRR13434680_qc_fHP_2
        23.1%
        47%
        148 bp
        24.6
        SRR13434681_qc_fHP_1
        26.5%
        50%
        150 bp
        29.6
        SRR13434681_qc_fHP_2
        25.2%
        50%
        150 bp
        29.6
        SRR13434686_qc_fHP_1
        72.5%
        44%
        150 bp
        45.4
        SRR13434686_qc_fHP_2
        70.2%
        44%
        150 bp
        45.4
        SRR13434687_qc_fHP_1
        22.7%
        52%
        150 bp
        35.9
        SRR13434687_qc_fHP_2
        21.7%
        52%
        144 bp
        35.9
        SRR13434688_qc_fHP_1
        40.0%
        50%
        150 bp
        31.7
        SRR13434688_qc_fHP_2
        38.1%
        50%
        150 bp
        31.7
        SRR13434689_qc_fHP_1
        13.4%
        50%
        150 bp
        27.1
        SRR13434689_qc_fHP_2
        12.7%
        50%
        150 bp
        27.1
        SRR13434690_qc_fHP_1
        18.1%
        49%
        150 bp
        30.1
        SRR13434690_qc_fHP_2
        17.2%
        49%
        148 bp
        30.1
        SRR13434691_qc_fHP_1
        14.2%
        51%
        150 bp
        24.8
        SRR13434691_qc_fHP_2
        13.6%
        51%
        146 bp
        24.8
        SRR13434692_qc_fHP_1
        16.7%
        48%
        150 bp
        24.4
        SRR13434692_qc_fHP_2
        15.8%
        48%
        150 bp
        24.4
        SRR13434693_qc_fHP_1
        30.9%
        50%
        150 bp
        26.2
        SRR13434693_qc_fHP_2
        29.6%
        50%
        150 bp
        26.2
        SRR13434694_qc_fHP_1
        32.4%
        50%
        150 bp
        33.1
        SRR13434694_qc_fHP_2
        30.7%
        50%
        148 bp
        33.1
        SRR13434695_qc_fHP_1
        12.7%
        46%
        150 bp
        12.4
        SRR13434695_qc_fHP_2
        11.6%
        46%
        150 bp
        12.4
        SRR13434697_qc_fHP_1
        18.1%
        49%
        150 bp
        13.0
        SRR13434697_qc_fHP_2
        16.5%
        49%
        150 bp
        13.0
        SRR13434698_qc_fHP_1
        8.4%
        51%
        150 bp
        12.7
        SRR13434698_qc_fHP_2
        7.7%
        51%
        150 bp
        12.7
        SRR13434699_qc_fHP_1
        12.9%
        52%
        150 bp
        16.9
        SRR13434699_qc_fHP_2
        11.9%
        52%
        148 bp
        16.9
        SRR13434700_qc_fHP_1
        16.4%
        48%
        150 bp
        14.9
        SRR13434700_qc_fHP_2
        15.4%
        48%
        150 bp
        14.9
        SRR13434701_qc_fHP_1
        17.5%
        48%
        150 bp
        13.7
        SRR13434701_qc_fHP_2
        16.7%
        48%
        150 bp
        13.7
        SRR13434702_qc_fHP_1
        17.5%
        49%
        150 bp
        12.7
        SRR13434702_qc_fHP_2
        16.5%
        49%
        150 bp
        12.7
        SRR13434703_qc_fHP_1
        14.2%
        48%
        150 bp
        17.0
        SRR13434703_qc_fHP_2
        13.2%
        48%
        150 bp
        17.0
        SRR13434704_qc_fHP_1
        16.9%
        49%
        146 bp
        19.3
        SRR13434704_qc_fHP_2
        16.2%
        49%
        134 bp
        19.3
        SRR13434705_qc_fHP_1
        6.7%
        49%
        150 bp
        7.4
        SRR13434705_qc_fHP_2
        6.3%
        49%
        144 bp
        7.4
        SRR13434706_qc_fHP_1
        11.0%
        50%
        132 bp
        21.0
        SRR13434706_qc_fHP_2
        10.9%
        50%
        124 bp
        21.0
        SRR13434708_qc_fHP_1
        22.1%
        48%
        150 bp
        16.0
        SRR13434708_qc_fHP_2
        21.3%
        48%
        138 bp
        16.0
        SRR13434709_qc_fHP_1
        14.2%
        51%
        150 bp
        10.9
        SRR13434709_qc_fHP_2
        13.4%
        51%
        138 bp
        10.9
        SRR13434710_qc_fHP_1
        22.6%
        50%
        150 bp
        18.8
        SRR13434710_qc_fHP_2
        21.5%
        50%
        144 bp
        18.8
        SRR13434711_qc_fHP_1
        10.7%
        50%
        150 bp
        21.3
        SRR13434711_qc_fHP_2
        10.5%
        50%
        138 bp
        21.3
        SRR13434712_qc_fHP_1
        13.2%
        50%
        150 bp
        15.8
        SRR13434712_qc_fHP_2
        12.6%
        50%
        140 bp
        15.8
        SRR13434713_qc_fHP_1
        20.8%
        50%
        150 bp
        15.4
        SRR13434713_qc_fHP_2
        20.0%
        50%
        150 bp
        15.4
        SRR13434714_qc_fHP_1
        10.5%
        49%
        150 bp
        15.5
        SRR13434714_qc_fHP_2
        10.1%
        49%
        138 bp
        15.5
        SRR13434715_qc_fHP_1
        11.3%
        48%
        142 bp
        16.5
        SRR13434715_qc_fHP_2
        11.0%
        48%
        136 bp
        16.5
        SRR13434716_qc_fHP_1
        16.7%
        49%
        150 bp
        17.5
        SRR13434716_qc_fHP_2
        16.3%
        49%
        138 bp
        17.5
        SRR13434717_qc_fHP_1
        15.4%
        49%
        150 bp
        18.3
        SRR13434717_qc_fHP_2
        14.8%
        49%
        140 bp
        18.3

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        loading..

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        loading..

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        loading..

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        loading..

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        loading..

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.